\r
import compbio.engine.client.CommandBuilder.Parameter;\r
import compbio.engine.conf.PropertyHelperManager;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitsManager;\r
import compbio.util.PropertyHelper;\r
import compbio.util.Util;\r
\r
public abstract class SkeletalExecutable<T> implements Executable<T> {\r
\r
- protected static final PropertyHelper ph = PropertyHelperManager\r
- .getPropertyHelper();\r
+ protected static final PropertyHelper ph = PropertyHelperManager\r
+ .getPropertyHelper();\r
\r
- private static Logger log = Logger.getLogger(SkeletalExecutable.class);\r
+ private static Logger log = Logger.getLogger(SkeletalExecutable.class);\r
\r
- protected String inputFile = "input.txt";\r
- protected String outputFile = "output.txt";\r
- protected String errorFile = "error.txt";\r
+ // Cache for Limits information\r
+ private LimitsManager<T> limits;\r
\r
- private boolean isInputSet = false;\r
- private boolean isOutputSet = false;\r
- private boolean isErrorSet = false;\r
+ protected String inputFile = "input.txt";\r
+ protected String outputFile = "output.txt";\r
+ protected String errorFile = "error.txt";\r
\r
- /**\r
- * This has to allow duplicate parameters as different options may have the\r
- * same value e.g. Muscle -weight1 clustalw -weight2 clustalw\r
- */\r
- protected CommandBuilder<T> cbuilder;\r
+ private boolean isInputSet = false;\r
+ private boolean isOutputSet = false;\r
+ private boolean isErrorSet = false;\r
\r
- public SkeletalExecutable() {\r
- cbuilder = new CommandBuilder<T>(" ");\r
- }\r
+ /**\r
+ * This has to allow duplicate parameters as different options may have the\r
+ * same value e.g. Muscle -weight1 clustalw -weight2 clustalw\r
+ */\r
+ protected CommandBuilder<T> cbuilder;\r
+\r
+ public SkeletalExecutable() {\r
+ cbuilder = new CommandBuilder<T>(" ");\r
+ }\r
\r
- public SkeletalExecutable(String parameterKeyValueDelimiter) {\r
- assert parameterKeyValueDelimiter != null;\r
- cbuilder = new CommandBuilder<T>(parameterKeyValueDelimiter);\r
- }\r
+ public SkeletalExecutable(String parameterKeyValueDelimiter) {\r
+ assert parameterKeyValueDelimiter != null;\r
+ cbuilder = new CommandBuilder<T>(parameterKeyValueDelimiter);\r
+ }\r
\r
- public SkeletalExecutable<T> setInput(String inFile) {\r
- if (compbio.util.Util.isEmpty(inFile)) {\r
- throw new IllegalArgumentException("Input file must not be NULL");\r
+ public SkeletalExecutable<T> setInput(String inFile) {\r
+ if (compbio.util.Util.isEmpty(inFile)) {\r
+ throw new IllegalArgumentException("Input file must not be NULL");\r
+ }\r
+ this.inputFile = inFile;\r
+ this.isInputSet = true;\r
+ return this;\r
}\r
- this.inputFile = inFile;\r
- this.isInputSet = true;\r
- return this;\r
- }\r
-\r
- public SkeletalExecutable<T> setOutput(String outFile) {\r
- if (compbio.util.Util.isEmpty(outFile)\r
- || PathValidator.isAbsolutePath(outFile)) {\r
- throw new IllegalArgumentException(\r
- "Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
- + outFile);\r
+\r
+ public SkeletalExecutable<T> setOutput(String outFile) {\r
+ if (compbio.util.Util.isEmpty(outFile)\r
+ || PathValidator.isAbsolutePath(outFile)) {\r
+ throw new IllegalArgumentException(\r
+ "Output file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
+ + outFile);\r
+ }\r
+ this.outputFile = outFile;\r
+ this.isOutputSet = true;\r
+ return this;\r
}\r
- this.outputFile = outFile;\r
- this.isOutputSet = true;\r
- return this;\r
- }\r
-\r
- public SkeletalExecutable<T> setError(String errFile) {\r
- if (compbio.util.Util.isEmpty(errFile)\r
- || PathValidator.isAbsolutePath(errFile)) {\r
- throw new IllegalArgumentException(\r
- "Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
- + errFile);\r
+\r
+ public SkeletalExecutable<T> setError(String errFile) {\r
+ if (compbio.util.Util.isEmpty(errFile)\r
+ || PathValidator.isAbsolutePath(errFile)) {\r
+ throw new IllegalArgumentException(\r
+ "Error file must not be NULL and Absolute path could not be used! Please provide the filename only. Value provided: "\r
+ + errFile);\r
+ }\r
+ this.errorFile = errFile;\r
+ this.isErrorSet = true;\r
+ return this;\r
+ }\r
+\r
+ @Override\r
+ public CommandBuilder<T> getParameters(ExecProvider provider) {\r
+ /*\r
+ * Prevent modification of the parameters unintentionally. This is\r
+ * important to preserve executable parameters intact as engine could\r
+ * add things into the array as it see fit. For instance\r
+ * ExecutableWrapper (part of local engines) add command line as the\r
+ * first element of an array.\r
+ */\r
+ paramValueUpdater();\r
+ return cbuilder;\r
+ }\r
+\r
+ @Override\r
+ public Executable<T> addParameters(List<String> parameters) {\r
+ cbuilder.addParams(parameters);\r
+ return this;\r
+ }\r
+\r
+ public Executable<T> setParameter(String parameter) {\r
+ cbuilder.setParam(parameter);\r
+ return this;\r
}\r
- this.errorFile = errFile;\r
- this.isErrorSet = true;\r
- return this;\r
- }\r
-\r
- @Override\r
- public CommandBuilder<T> getParameters(ExecProvider provider) {\r
- /*\r
- * Prevent modification of the parameters unintentionally. This is\r
- * important to preserve executable parameters intact as engine could\r
- * add things into the array as it see fit. For instance\r
- * ExecutableWrapper (part of local engines) add command line as the\r
- * first element of an array.\r
+\r
+ /**\r
+ * This is a generic method of changing values of the parameters with\r
+ * properties\r
+ * \r
+ * This method iterates via commands for an executable finding matches from\r
+ * the Executable.properties file and replacing values in CommandBuilder\r
+ * with a combination of value from CommandBuilder to merge path from\r
+ * properties\r
*/\r
- paramValueUpdater();\r
- return cbuilder;\r
- }\r
-\r
- @Override\r
- public Executable<T> addParameters(List<String> parameters) {\r
- cbuilder.addParams(parameters);\r
- return this;\r
- }\r
-\r
- public Executable<T> setParameter(String parameter) {\r
- cbuilder.setParam(parameter);\r
- return this;\r
- }\r
-\r
- /**\r
- * This is a generic method of changing values of the parameters with\r
- * properties\r
- * \r
- * This method iterates via commands for an executable finding matches from\r
- * the Executable.properties file and replacing values in CommandBuilder\r
- * with a combination of value from CommandBuilder to merge path from\r
- * properties\r
- */\r
- void paramValueUpdater() {\r
- for (Parameter command : cbuilder.getCommandList()) {\r
- if (command.value == null) {\r
- continue;\r
- }\r
- String propertyPath = compbio.engine.client.Util.getExecProperty(\r
- command.name + ".path", getType());\r
- if (Util.isEmpty(propertyPath)) {\r
- continue;\r
- }\r
- if (new File(command.value).isAbsolute()) {\r
- // Matrix can be found so no actions necessary\r
- // This method has been called already and the matrix name\r
- // is modified to contain full path // no further actions is\r
- // necessary\r
- continue;\r
- }\r
- String absMatrixPath = compbio.engine.client.Util\r
- .convertToAbsolute(propertyPath);\r
- command.value = absMatrixPath + File.separator + command.value;\r
- cbuilder.setParam(command);\r
+ void paramValueUpdater() {\r
+ for (Parameter command : cbuilder.getCommandList()) {\r
+ if (command.value == null) {\r
+ continue;\r
+ }\r
+ String propertyPath = compbio.engine.client.Util.getExecProperty(\r
+ command.name + ".path", getType());\r
+ if (Util.isEmpty(propertyPath)) {\r
+ continue;\r
+ }\r
+ if (new File(command.value).isAbsolute()) {\r
+ // Matrix can be found so no actions necessary\r
+ // This method has been called already and the matrix name\r
+ // is modified to contain full path // no further actions is\r
+ // necessary\r
+ continue;\r
+ }\r
+ String absMatrixPath = compbio.engine.client.Util\r
+ .convertToAbsolute(propertyPath);\r
+ command.value = absMatrixPath + File.separator + command.value;\r
+ cbuilder.setParam(command);\r
+ }\r
}\r
- }\r
-\r
- /**\r
- * This method cannot really tell whether the files has actually been\r
- * created or not. It must be overridden as required.\r
- * \r
- * @see compbio.engine.client.Executable#getCreatedFiles()\r
- */\r
- @Override\r
- public List<String> getCreatedFiles() {\r
- return Arrays.asList(getOutput(), getError());\r
- }\r
-\r
- @Override\r
- public String getInput() {\r
- return inputFile;\r
- }\r
-\r
- protected boolean isInputSet() {\r
- return isInputSet;\r
- }\r
-\r
- protected boolean isOutputSet() {\r
- return isOutputSet;\r
- }\r
-\r
- protected boolean isErrorSet() {\r
- return isErrorSet;\r
- }\r
-\r
- @Override\r
- public String getOutput() {\r
- return outputFile;\r
- }\r
-\r
- @Override\r
- public String getError() {\r
- return errorFile;\r
- }\r
-\r
- @Override\r
- public String toString() {\r
- String value = "Input: " + this.getInput() + "\n";\r
- value += "Output: " + this.getOutput() + "\n";\r
- value += "Error: " + this.getError() + "\n";\r
- value += "Class: " + this.getClass() + "\n";\r
- value += "Params: " + cbuilder + "\n";\r
- return value;\r
- }\r
-\r
- @Override\r
- public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {\r
- if (!compbio.util.Util.isEmpty(rconfig.getOutput())) {\r
- setOutput(rconfig.getOutput());\r
+\r
+ /**\r
+ * This method cannot really tell whether the files has actually been\r
+ * created or not. It must be overridden as required.\r
+ * \r
+ * @see compbio.engine.client.Executable#getCreatedFiles()\r
+ */\r
+ @Override\r
+ public List<String> getCreatedFiles() {\r
+ return Arrays.asList(getOutput(), getError());\r
}\r
- if (!compbio.util.Util.isEmpty(rconfig.getError())) {\r
- setError(rconfig.getError());\r
+\r
+ @Override\r
+ public String getInput() {\r
+ return inputFile;\r
}\r
- if (!compbio.util.Util.isEmpty(rconfig.getInput())) {\r
- setInput(rconfig.getInput());\r
+\r
+ protected boolean isInputSet() {\r
+ return isInputSet;\r
}\r
- this.cbuilder = (CommandBuilder<T>) rconfig.getParameters();\r
- return this;\r
- }\r
-\r
- @Override\r
- public boolean equals(Object obj) {\r
- if (obj == null) {\r
- return false;\r
+\r
+ protected boolean isOutputSet() {\r
+ return isOutputSet;\r
}\r
- if (!(obj instanceof SkeletalExecutable<?>)) {\r
- return false;\r
+\r
+ protected boolean isErrorSet() {\r
+ return isErrorSet;\r
}\r
- SkeletalExecutable<?> exec = (SkeletalExecutable<?>) obj;\r
- if (!Util.isEmpty(this.inputFile) && !Util.isEmpty(exec.inputFile)) {\r
- if (!this.inputFile.equals(exec.inputFile)) {\r
- return false;\r
- }\r
+\r
+ @Override\r
+ public String getOutput() {\r
+ return outputFile;\r
}\r
- if (!Util.isEmpty(this.outputFile) && !Util.isEmpty(exec.outputFile)) {\r
- if (!this.outputFile.equals(exec.outputFile)) {\r
- return false;\r
- }\r
+\r
+ @Override\r
+ public String getError() {\r
+ return errorFile;\r
}\r
- if (!Util.isEmpty(this.errorFile) && !Util.isEmpty(exec.errorFile)) {\r
- if (!this.errorFile.equals(exec.errorFile)) {\r
- return false;\r
- }\r
+\r
+ @Override\r
+ public String toString() {\r
+ String value = "Input: " + this.getInput() + "\n";\r
+ value += "Output: " + this.getOutput() + "\n";\r
+ value += "Error: " + this.getError() + "\n";\r
+ value += "Class: " + this.getClass() + "\n";\r
+ value += "Params: " + cbuilder + "\n";\r
+ return value;\r
}\r
- if (!this.cbuilder.equals(exec.cbuilder)) {\r
- return false;\r
+\r
+ @Override\r
+ public Executable<?> loadRunConfiguration(RunConfiguration rconfig) {\r
+ if (!compbio.util.Util.isEmpty(rconfig.getOutput())) {\r
+ setOutput(rconfig.getOutput());\r
+ }\r
+ if (!compbio.util.Util.isEmpty(rconfig.getError())) {\r
+ setError(rconfig.getError());\r
+ }\r
+ if (!compbio.util.Util.isEmpty(rconfig.getInput())) {\r
+ setInput(rconfig.getInput());\r
+ }\r
+ this.cbuilder = (CommandBuilder<T>) rconfig.getParameters();\r
+ return this;\r
+ }\r
+\r
+ @Override\r
+ public boolean equals(Object obj) {\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+ if (!(obj instanceof SkeletalExecutable<?>)) {\r
+ return false;\r
+ }\r
+ SkeletalExecutable<?> exec = (SkeletalExecutable<?>) obj;\r
+ if (!Util.isEmpty(this.inputFile) && !Util.isEmpty(exec.inputFile)) {\r
+ if (!this.inputFile.equals(exec.inputFile)) {\r
+ return false;\r
+ }\r
+ }\r
+ if (!Util.isEmpty(this.outputFile) && !Util.isEmpty(exec.outputFile)) {\r
+ if (!this.outputFile.equals(exec.outputFile)) {\r
+ return false;\r
+ }\r
+ }\r
+ if (!Util.isEmpty(this.errorFile) && !Util.isEmpty(exec.errorFile)) {\r
+ if (!this.errorFile.equals(exec.errorFile)) {\r
+ return false;\r
+ }\r
+ }\r
+ if (!this.cbuilder.equals(exec.cbuilder)) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ @Override\r
+ public int hashCode() {\r
+ int code = inputFile.hashCode();\r
+ code += outputFile.hashCode();\r
+ code += errorFile.hashCode();\r
+ code *= this.cbuilder.hashCode();\r
+ return code;\r
+ }\r
+\r
+ public String getClusterSettings() {\r
+ String settings = ph.getProperty(getType().getSimpleName()\r
+ .toLowerCase() + ".cluster.settings");\r
+ return settings == null ? "" : settings;\r
}\r
- return true;\r
- }\r
-\r
- @Override\r
- public int hashCode() {\r
- int code = inputFile.hashCode();\r
- code += outputFile.hashCode();\r
- code += errorFile.hashCode();\r
- code *= this.cbuilder.hashCode();\r
- return code;\r
- }\r
-\r
- public String getClusterSettings() {\r
- String settings = ph.getProperty(getType().getSimpleName()\r
- .toLowerCase()\r
- + ".cluster.settings");\r
- return settings == null ? "" : settings;\r
- }\r
-\r
- /**\r
+\r
+ /**\r
* \r
* @return number of cpus to use on the cluster or 0 if the value is\r
* undefined\r
*/\r
public static int getClusterCpuNum(Class<? extends Executable<?>> type) {\r
int cpus = 0;\r
- String cpuNum = ph.getProperty(type.getSimpleName().toLowerCase()+ ".cluster.cpunum");\r
+ String cpuNum = ph.getProperty(type.getSimpleName().toLowerCase()\r
+ + ".cluster.cpunum");\r
if (compbio.util.Util.isEmpty(cpuNum)) {\r
return 0;\r
}\r
cpus = Integer.parseInt(cpuNum);\r
} catch (NumberFormatException e) {\r
// safe to ignore\r
- log\r
- .debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: "\r
+ log.debug("Number of cpus to use for cluster execution is defined but could not be parsed as integer! Given value is: "\r
+ cpuNum);\r
return 0;\r
}\r
if (cpus < 1 || cpus > 100) {\r
throw new InvalidParameterException(\r
"Number of cpu for cluster execution must be within 1 and 100! "\r
- + "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is "\r
- + cpus);\r
+ + "Look at the value of 'tcoffee.cluster.cpunum' property. Given value is "\r
+ + cpus);\r
}\r
return cpus;\r
}\r
\r
- public abstract Class<? extends Executable<?>> getType();\r
+ @Override\r
+ public Limit<T> getLimit(String presetName) {\r
+\r
+ if (limits == null) {\r
+ limits = getLimits();\r
+ }\r
+\r
+ Limit<T> limit = null;\r
+ if (limits != null) {\r
+ // this returns default limit if preset is undefined!\r
+ limit = limits.getLimitByName(presetName);\r
+ }\r
+ // If limit is not defined for a particular preset, then return default\r
+ // limit\r
+ if (limit == null) {\r
+ log.debug("Limit for the preset " + presetName\r
+ + " is not found. Using default");\r
+ limit = limits.getDefaultLimit();\r
+ }\r
+ return limit;\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<T> getLimits() {\r
+ synchronized (SkeletalExecutable.class) {\r
+ if (limits == null) {\r
+ limits = compbio.runner.Util.getLimits(this.getType());\r
+ }\r
+ }\r
+ return limits;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return subclasses must return their type\r
+ */\r
+ public abstract Class<Executable<T>> getType();\r
\r
}\r
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